To cite RStan in publications use:

Stan Development Team (2016). RStan: the R interface to Stan. R package version 2.14.1. http://mc-stan.org/.

Corresponding BibTeX entry:

  @Misc{,
    title = {{RStan}: the {R} interface to {Stan}},
    author = {{Stan Development Team}},
    note = {R package version 2.14.1},
    year = {2016},
    url = {http://mc-stan.org/},
  }